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SystemsGenetics / GEMmaker

A workflow for construction of Gene Expression count Matrices (GEMs). Useful for Differential Gene Expression (DGE) analysis and Gene Co-Expression Network (GCN) construction
https://gemmaker.readthedocs.io/en/latest/
MIT License
33 stars 16 forks source link

GEMmaker no longer creates nextflow reports by default #267

Open JohnHadish opened 1 year ago

JohnHadish commented 1 year ago

Description of feature

GEMmaker used to automatically produce the summary, timeline, and trace reports by default. The user must now request these to be run manually.

GEMmaker Documentation on Reports Nextflow Documentation

What needs to be added back in:

trace {
    enabled = true
    file = 'pipeline_trace.txt'
    fields = 'task_id,name,status,exit,realtime,%cpu,rss'
}
spficklin commented 1 year ago

I recently ran GEMmaker and got these files in the results/pipeline_info directory:

execution_report_2022-11-06_16-53-56.html    
execution_trace_2022-11-06_16-53-56.txt
execution_timeline_2022-11-06_16-53-56.html  
pipeline_dag_2022-11-06_16-53-56.svg

Are these the files you are missing?

JohnHadish commented 1 year ago

Yes, those are the missing files. Do you have your submission script for that run?

spficklin commented 1 year ago

Yes, I do. I'll send them to you. I didn't include the trace settings above.